Avery Tools made a nice tool to do this job -
The hex portion shown in the pic is threaded onto the end of the L-shaped pin. It creates an easy handle to get the pin inserted, and then handle portion can then be removed leaving the short pin in the hinge. The kit came with 6 hinge pins and is really easy to use.
Because the L-shaped pin is short you can rotate it clear of the skin slot and do a control surface full swing test for tightness when all of the pins are inserted.
It seems like no one is making this any more - glad I got mine.